A lithographic apparatus is a machine that applies a desired pattern onto a substrate, usually onto a target portion of the substrate. A lithographic apparatus can be used, for example, in the manufacture of integrated circuits (ICs). In that instance, a patterning device, which is alternatively referred to as a mask or a reticle, may be used to generate a circuit pattern to be formed on an individual layer of the IC. This pattern can be transferred onto a target portion (e.g. comprising part of, one, or several dies) on a substrate (e.g. a silicon wafer). Transfer of the pattern is typically via imaging onto a layer of radiation-sensitive material (resist) provided on the substrate. In general, a single substrate will contain a network of adjacent target portions that are successively patterned. Known lithographic apparatus include so-called steppers, in which each target portion is irradiated by exposing an entire pattern onto the target portion at one time, and so-called scanners, in which each target portion is irradiated by scanning the pattern through a radiation beam in a given direction (the “scanning”-direction) while synchronously scanning the substrate parallel or anti-parallel to this direction. It is also possible to transfer the pattern from the patterning device to the substrate by imprinting the pattern onto the substrate.
Alignment of a substrate relative to a projection system or a patterning device and other process control procedures can be carried by reference to optical measurements of metrology marks (such as alignment marks). For example, an optical measurement system may be provided to reflect radiation from one or more metrology marks formed on the substrate or patterning device. Periodic alignment marks, such as gratings, may be used, for example, and the position determined by reference to a center of symmetry or other characteristic property of the grating. Processing of the substrate can distort the metrology marks, which can make it difficult for the optical measurement system to operate effectively. For example, where alignment marks are being measured, the distortion may compromise determination of the alignment mark position. Calculating how reflected radiation may change due to the distortion may be time consuming and expensive.